Send FreeSurfer examples to Queens
lassoan opened this issue · 4 comments
As discussed here, FreeSurfer data export and/or import in Slicer is not fully correct. Need to provide example files and description what is not correct and how can be fixed.
Here is a link to an MRB File (100MB) containing the original T1, the output from freesurfer (Brain.finalsurfs.mgz), and two volumes (models) in freesurfer.
https://www.dropbox.com/sh/f2dcp3arcg0vlxz/AADNY-r1OShnQ-seGgM73iEOa?dl=0
The two volume models should be at the white matter / gray matter interface. If you use slice representation of the model (or convert to labelmap), you will find that there is a mismatch.
To identify the difference, we use at the command line (assumes freesurfer installed).
mri_info --vox2ras-tkr brain.finalsurfs.mgz
to identify the coordinates that freesurfer uses. We then enter these coordinates into the volume module in Slicer which then aligns the volume to the model.
Note that centering the volume (in the volume module) is almost but not exactly right.
This link is (somewhat) helpful - it details the coordinates from FS,
@Sunderlandkyl please check the data set and let me know if you need help with figuring out what the issue could be.
@jarrett-rushmore Could you upload the original freesurfer models before they are imported into Slicer?
@Sunderlandkyl Done, sir. In dropbox.